Variant rs1142326 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7

The NM_002122.5(HLA-DQA1):c.208C>A(p.Arg70Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0015 ( 1 hom., cov: 13)

Exomes 𝑓: 0.0034 ( 393 hom. )

Failed GnomAD Quality Control

Consequence

HLA-DQA1
NM_002122.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.255

Variant links:

Genes affected

HLA-DQA1 (HGNC:4942): (major histocompatibility complex, class II, DQ alpha 1) HLA-DQA1 belongs to the HLA class II alpha chain paralogues. The class II molecule is a heterodimer consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B Lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa. It is encoded by 5 exons; exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, and exon 4 encodes the transmembrane domain and the cytoplasmic tail. Within the DQ molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to four different molecules. Typing for these polymorphisms is routinely done for bone marrow transplantation. [provided by RefSeq, Jul 2008]

HLA-DQA1 links:

HLA-DQA1 (HGNC:):

HLA-DQA1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP7

Synonymous conserved (PhyloP=-0.255 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DQA1	NM_002122.5 linkuse as main transcript	c.208C>A	p.Arg70Arg	synonymous_variant	2/5	ENST00000343139.11	NP_002113.2	P01909A0A173ADG5Q8MH44
HLA-DQA1	XM_006715079.5 linkuse as main transcript	c.208C>A	p.Arg70Arg	synonymous_variant	2/4		XP_006715142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DQA1	ENST00000343139.11 linkuse as main transcript	c.208C>A	p.Arg70Arg	synonymous_variant	2/5	6	NM_002122.5	ENSP00000339398.5		P01909

Frequencies

GnomAD3 genomes

AF:

0.00148

AC:

114

AN:

77196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00147

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00129

Gnomad ASJ

AF:

0.00118

Gnomad EAS

AF:

0.000780

Gnomad SAS

AF:

0.00168

Gnomad FIN

AF:

0.000690

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00170

Gnomad OTH

AF:

0.00211

GnomAD3 exomes

AF:

0.0107

AC:

1799

AN:

167538

Hom.:

151

AF XY:

0.0110

AC XY:

1006

AN XY:

91660

show subpopulations

Gnomad AFR exome

AF:

0.0147

Gnomad AMR exome

AF:

0.00709

Gnomad ASJ exome

AF:

0.0127

Gnomad EAS exome

AF:

0.00509

Gnomad SAS exome

AF:

0.00965

Gnomad FIN exome

AF:

0.00393

Gnomad NFE exome

AF:

0.0135

Gnomad OTH exome

AF:

0.00823

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00342

AC:

3154

AN:

923200

Hom.:

393

Cov.:

AF XY:

0.00400

AC XY:

1857

AN XY:

464830

show subpopulations

Gnomad4 AFR exome

AF:

0.00317

Gnomad4 AMR exome

AF:

0.0107

Gnomad4 ASJ exome

AF:

0.00818

Gnomad4 EAS exome

AF:

0.00174

Gnomad4 SAS exome

AF:

0.00829

Gnomad4 FIN exome

AF:

0.00186

Gnomad4 NFE exome

AF:

0.00279

Gnomad4 OTH exome

AF:

0.00337

GnomAD4 genome

AF:

0.00148

AC:

114

AN:

77282

Hom.:

Cov.:

AF XY:

0.00157

AC XY:

AN XY:

37594

show subpopulations

Gnomad4 AFR

AF:

0.00147

Gnomad4 AMR

AF:

0.00129

Gnomad4 ASJ

AF:

0.00118

Gnomad4 EAS

AF:

0.000784

Gnomad4 SAS

AF:

0.00168

Gnomad4 FIN

AF:

0.000690

Gnomad4 NFE

AF:

0.00170

Gnomad4 OTH

AF:

0.00206

Alfa

AF:

0.0238

Hom.:

319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

2.1

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over